What You Remember
by tripwasmyhero2161
Summary: PostCritical Mass. Shweir. John loses his memory nd Elizabeth must help him find it. Chapter 3 is completed. Please R&R!
1. Chapter 1

DISCLAIMER: I do NOT own Stargate Atlantis or anything Stargate affiliated. I can always wish, but we all know that will never happen.

This couldn't be done without the help and opinions of my friend and new gate fan, Antoinette. She helped me out when I was stuck. Her screen name on is pointy objects, y'all should check out her writing, its really good.

This actually started as a one-chapter ficlet, but has turned into a multi-chapter life story of romance.

SPOILERS: Post-Conversion

What You Remember

After Ronan Dex found out some of his people were still alive, he went in search for more survivors. It just happened to be in the same area as Colonel Sheppard and Teyla had some trading business.

After trading and Ronan's quest to find the remainder of his people, the puddle jumper held Dr. Rodney McKay, Lt. Colonel John Sheppard, Teyla Emmagan, and Ronan Dex. They were being chased by the Wraith. They were always feeding, but they must have had a hive ship in the area.

The Wraith still had no idea that Atlantis or the Athosian people were still there. No ships have been near Atlantis in months.

"More ships are coming. They'll be on my tail in a minute." Sheppard yelled. The puddle jumper was approaching a stargate. "Teyla, dial the gate."

The puddle jumper went through the gate. It closed right behind the jumper. As the jumper went through, the jumper was hit. The four passengers were hit hard.

_ShweirShweirShweir_

Dr. Elizabeth Weir, the head of the expedition, was waiting for the group to return.

The jumper came through the gate. It was raised into the jumper bay. Dr. Weir got to the room as quickly as possible.

As the hatch opened, Teyla and Ronan were the first out. Ronan supported Teyla as they walked.

"How'd it go?" Dr. Weir asked.

"We had some trouble." Teyla said.

"What trouble? The Wraith?" The doctor asked, as she looked them over. They both had bruises and cuts from the attack.

"Yeah, I don't think they followed us though. They'd be here by now." Ronan said.

"Good." She said to Ronan. Then turned to her headset.

"Carson, we have wounded. We need you down here now!" Dr. Weir said.

"Ah, I'll be there in a minute." Dr. Carson Beckett, the chief medical doctor, said.

"Now, Carson!" Dr. Weir demanded.

"Okay." He said.

Dr. Beckett came running in. he saw Teyla and Ronan first. He sent them to the infirmary.

Rodney, who was standing and talking, more like complaining to Dr. Weir, finally went to see Carson.

Carson checked over Rodney. "Dr. McKay, except for a few cuts and bruises, you're fine. You should go to the infirmary, just to double check."

"Yeah, you're probably right." Rodney said.

Rodney was finally leaving after complaining he was dying.

The medical team had brought Colonel Sheppard out on a stretcher. He was still unconscious.

_ShweirShweirShweir_

Rodney had been released from the infirmary. He was back in his lab.

"Rodney. Back to work, I see." Dr. Weir said.

"Well, I just couldn't stay away." Rodney said returning to his work.

"Have you come up with any reason for the Wraith attack?" Dr. Weir asked realizing how stupid the question was as soon as it left her mouth.

"Well, it could be the fact that they were feeding." Rodney said sarcastically.

"I know, stupid question." Dr. Weir said. "can you come up with a detector to alert us of the Wraith sooner?"

"You want me to upgrade a technology that we only have a minimum understanding of?" Rodney asked.

"Yes." She said simply.

"I'll figure out something." Rodney said.

"Thank you Rodney." She said. "I'll ask Dr. Zelanka to help you."

"Zelanka?" I don't need his help." Rodney complained.

"Do you want me to remind you of the help he's given you?" she said reminding him of his past.

"If he must help." Rodney gave in.

Elizabeth left the lab. She was going to return to her office, but ended up in the infirmary.

"How is he?" she asked Carson.

"I've run some test." Carson asked. He hated being the bearer of bad news, but it came with the job. "He has severe trauma to the head. I'm not really sure of his condition until he wakes up. That is, if he wakes up."

"If he wakes up?" she asked.

"He might be in a coma. The damage to the brain was too severe." Carson explained.

"I want to know the second he wakes up or if there are any changes in his condition." Dr. Weir said on her way out.

_ShweirShweirShweir_

John Sheppard opened his eyes. He looked around at his surrounding.

'Where am I?' he thought.

Carson was coming to check on John. He saw he was awake.

"Colonel, I'm glad you're awake." Carson said.

"Who? Where am I? Why am I here?" John yelled. He tried to get up to leave, but Carson yelled for a medical team to restrain him. "Why are you holding me here?"

"Do you remember anything about yourself?" Carson asked.

"No." John yelled angry.

"Dr. Weir had been called by Carson. She had reached the infirmary. She saw John awake, but he was still being restrained.

"How is he?" she asked.

"He's awake, but is aggressive and he has amnesia." Carson explained Colonel Sheppard's condition.

"Is there any chance of recovery?" Dr. Weir asked.

"There have been cases where the memory is recovered, but there have been only few cases." Carson said.

"Carson, we need John! Can this be done?" Dr. Weir asked.

"Theoretically, yes, but the chances—" Carson was cut off.

"The chances don't matter. As long as his memory returns." Dr. Weir demanded. "Use anything and anyone if you need it."

Dr. Weir walked towards the door.

"Elizabeth." She heard her name.

She turned to face the person who called her name.

"Do you know who I am?" She asked.

"Yes." He said simply.

"Do you know where you are?" She asked.

"No." he said. He was clam since Elizabeth had been in the infirmary.

"Do you know anything about yourself or what you do here?" She asked.

"No." John replied.

"Did you hear my name anywhere?" Elizabeth asked.

"No." He said.

"How do you know who I am?" She asked.

"I've seen you. I guess while I was unconscious. I saw you." John explained.

"In your dreams?" She asked.

"You could say that." He said. A grin formed on his face.

"We're going to get you as good as new." She said with a warm smile. She placed his hand on top of his and gave it a quick squeeze before leaving.

_ShweirShweirShweir_

Dr. Weir called Teyla to her office.

"How are you?" she asked.

"I am well." Teyla responded.

"I guess you have heard about Colonel Sheppard. Knowing the speed of rumors around here." Dr. Weir said.

"Yes." She said.

"I would like you to reintroduce him to the city. Reintroduce him to everyone." Dr. Weir asked.

"I will. Good Day, Dr. Weir." Teyla said.

"Good Day." She said softly. She returned to her reports.

_ShweirShweirShweir_

As asked by Dr. Weir, Teyla took John to the labs, the jumper bay, the gym, his quarters, and the cafeteria.

Rodney and Ronan were both eating when they arrived. They both had mountains of food on their plates.

Teyla and John got food and joined them.

"Hello Ronan, Rodney." Teyla greeted them. She gave Ronan a soft smile and returned to her food.

"John, so, are you feeling better?" Rodney asked.

"Huh?" John responded. He still wasn't use to hearing his own name.

"I asked how you're feeling." Rodney repeated himself. Then muttered, "the one time I try to be nice…" Then it got a bit clustered.

"Rodney, right?" John confirmed. Rodney nodded. "Does this food normally taste like lemon?"

"Citrus?" Rodney yelled in a high-pitched voice. He knocked over his chair. "Citrus? I'm highly allergic to citrus. Clear the way people." He ran to the infirmary.

"I don't know what possessed me to say that." John said.

"It was a memory, John." Teyla said. "Now that he is gone, we can eat peacefully."

After eating, they returned to the gym. Teyla handed a set of sticks to John.

"Now, as I showed you earlier." Teyla said. John remembered every move, exactly.

"It is getting late. You should return to your quarters." She said. John said nothing. She returned to his quarters.

He looked around. He saw all the things that were apparently his. He saw his Johnny Cash poster, his copy of War and Peace, and a tape sitting on the shelf. John picked up the tape. It was marked 'Superbowl.' It was the only thing on the shelf.

John went in search of somewhere to watch it. He did eventually find a place. There was a screen. He put the tape in. the game started. Elizabeth walked by. 'Football,' she thought/ she let out a quiet laugh. Next through her mind was 'Popcorn! All games need popcorn.' She went to find the remaining popcorn on Atlantis.

She did find some. After making it, she returned to the room John was in.

"I thought you would want this." Elizabeth said. She handed him the popcorn and sat down next to him.

He started eating the popcorn as if he remembered it. They were both watching the game, but they both did not understand it.

"I think I remember this." John said skeptically.

"You do?" Elizabeth asked.

"I was sitting here with Ford and Teyla. You were standing at the door." He remembered.

"Yes. That's right." She said. "See, your memory is coming back already."

"It seems so." He said. "Hey, can I ask you something?"

"Yeah, anything." She replied.

"Did we…I mean, were we…what I'm trying to say is…" Elizabeth cut him off.

"Did we have a relationship that was more than friends?" She finished his question.

"Yes." He said.

"No. We never did. We are the leaders. We couldn't have that relationship." She explained.

"Never once?" He asked.

"We're slowly being friends." Elizabeth said. In her mind, she remembered when the Iratus bug attacked him. She thought she was going to lose him forever, but never let it show. She could never imagine Atlantis without him. He wanted to tell her something, but couldn't bear to hear it. She just couldn't.

They continued to watch the game in silence.

The game eventually ended. John walked with Elizabeth to her quarters.

"This kind of felt like a date, didn't it?" John suggested.

"It was just a friendly thing. It wasn't really a date." She said.

"Elizabeth, we have to stop kidding ourselves." He started.

"John…" She started.

"Wait, let me finish before you say anything." He continued. "I know you say we never had a relationship because we were the leaders in this expedition, but I know how I feel, memory or no memory. And I'm pretty sure you feel the same way." He leaned into kiss her, but she pulled away. She entered her quarters and closed the door behind her.

John didn't take this as rejection. It was just Elizabeth not accepting her feelings.

As he walked to his quarters, he started to think. Memories were slowly returning to him. He remembered a few things, but they were strong memories. John was going to sleep on it before reporting to Carson in the morning.

'Hello.' Elizabeth said.

'Hi. What are you doing here?' John asked.

'I've come to help you.' She said.

'But how? Carson cant even help me.' He said.

'You haven't realized this yet, but this is a dream.' She explained.

'That explains it.' He said. "So, haw can you help me in reality or in the dream world?'

'I am the key to your memories. The only way you can retrieve your memory is through me.' She explained.

'But you rejected me.' John said.

'You must keep trying! I'll eventually come around.' She said. 'I must go, it will by daylight soon and you must see Carson in the morning.'

John woke the next morning. He went to see Carson.

"I've got it!" John proclaimed as he entered the infirmary.

"Colonel?" Carson was unsure of what was happening.

"I've figured it out!" John shouted.

"Well, Colonel, why don't we sit over here and you can tell me what you have figured out." Carson said calmly, leading John to one of the beds.

"I know how to get my memories back. I figured it out!" He said.

"Do you mind sharing with the class?" Carson asked.

"Elizabeth!" John said.

"Elizabeth? What about her?" He asked.

"She the link. She is the key to getting my memories back. I need her. no matter how long it takes." John explained.

"Colonel, you know what you're suggesting?" Carson questioned him.

"Yes, I do." He said with confidence. "I just wanted to run it by you first." John stood up. Before he made it to the infirmary doors, Carson stopped him.

"Are you sure you know what you're doing?" Carson asked again.

"Carson." John thought for a second to make sure he really knew what he was doing. "I know what I'm doing."

John went on his way. He was going to see Elizabeth, but Colonel Caldwell stopped him.

"Colonel. I see you're up and well." He said, pretending to be nice.

"Do I know you?" John asked.

"Yes, I'm Steven Caldwell. I've replaced you as Head of Security." He said.

John was about to say 'oh, but was cut off by a voice rounding the corner. She had heard what Caldwell had said.

"Colonel." She greeted him.

"Doctor." He greeted her.

"Shouldn't you be on your way to the Daedalus?" Dr. Weir asked.

"I was on my way before I ran into Colonel Sheppard." Caldwell explained.

"Well, you can continue on your way." She said.

Caldwell left.

"I hope he wasn't too much trouble." Elizabeth said.

"No, he was just telling me about helping me out as 'Head of Security.'" John explained.

"Head of Security? Caldwell?" Elizabeth asked, half laughing." I gave Head of Security to Major Lorne. Caldwell will never be Head of Security again."

"Why not?" John asked, curious.

"He changed everything." Elizabeth explained.

"Well, that's a good reason." He said.

There was a moment of silence between them.

"I was just coming to see you." He said. "I've figured you how to get my memories back."

"Okay. I'm listening." She said.

"You." He said.

"Me?" She questioned. "How am I going to help?"

"I don't know, but every time you're around, I start to remember things." He explained.

"Does it happen with anyone else around?" Elizabeth asked. she was trying to weasel her way out of her feelings.

"Well, there was the one time I reminded Rodney about citrus, but that was the only time it happened with other people around." He said. "It's actually kind of weird."

"I guess I can help, if it's the only way to get your memories back." She said.

"Carson did say it was going to take a long time before any memories returned." John said. It was true that John Sheppard had feeling for Elizabeth Weir, but at the moment, he just wanted his memories back. If she showed the same feelings in the process, that would be good too.

"What do we have to do?" Elizabeth said.

"I don't really know. I guess we could always go back to the places I'd normally go." He said.

"Okay. The gym, the cafeteria, the meeting room." She said, but then she thought 'your quarters,' she wanted to keep things professional. She also thought the balcony, but she wanted to stay in public places.

First, they went to the gym. It was the one place on Atlantis that John spent more of his time.

"Okay, anything yet?" She asked impatiently.

"No, It doesn't happen just like that. It takes time." John said. He picked up some sticks and started swinging them at an imaginary opponent. "Maybe some training will help me remember."

Elizabeth picked up some sticks. They both went into their starting stance. Elizabeth and John fought. He used his strength against her. She fought back equally. They both knocked each other to the ground a few times. Eventually, John over powered her.

He held her to the wall. There breaths intertwined. They stared into each other's eyes.

"I have the strange feeling that I've been here before." He said.

"You get around, then?" She asked.

"No, it's just…" He could say no more.

John dove in for a kiss. It all came back. All his memories, but he didn't tell her, not at that moment. He could use it to his advantage.

She was kissing back, but suddenly she broke the kiss off. They still were close.

"John, we can't do this." She said.

"Why not? We both want this." He asked.

"It's not appropriate." She responded. They put distance between each other.

"Maybe we should continue this tomorrow." She suggested. She could barely contain herself.

"No, we have time. Let's eat." He said.

"Yeah, I guess that would be okay." She said.

They used the transporter to go to the same level as the cafeteria. On the way, they talked. John made things uncomfortable.

"About earlier…" he trailed off.

"John, don't. Let's just put it behind us." She said.

"What if I don't want to put it behind us?" He questioned her. He stopped, but she kept walking until she realized that he had stopped.

"John? Why? It's not what you want. I'm not what you want." She said, now facing him.

"How do you know?" He asked.

"John." She said. "I know you want me to feel the same way, but I just can't. Your memories will tell you that."

"But I don't have them." He lied.

"What if it didn't work out? Would one of us have to go back to Earth?" She asked.

"How about we not think about that." John said. "Now, is it you can't admit you have feelings for my or is it you won't admit you have feelings for me?" he asked.

"John." She sighed. Elizabeth just walked away.

_ShweirShweirShweir_

A/N: What did you all think? Was it good?

What will happen? Will John finally tell Elizabeth about his memories? Will Elizabeth finally give in to her feelings?


	2. Chapter 2

Thank you to **Kyrah-Lee** (Lexa), **Jenna R**, and** Sheppardster **for the reviews.

**Kyrah-Lee**- I already have the second chapter written out all I have to do it type it up. I'm so glad you like it!

**Jenna R**- The chapters will keep coming.

**Sheppardster**- Thank you. I chapter will always come out as soon as possible.

Sorry about all the trouble with this chapter. I must have saved the wrong copy to the wrong document.

As I am typing this, I see that I have 453 hits since I posted at midnight on Saturday. That really makes me happy! But only three of those 453 hits have reviewed. Did you not like it? Was it that bad?

I don't know when Chapter 3 will be out. I'm frantically writing at this moment. Hopefully it will be out by February 10. I'm sorry for the wait.

Chapter 2

A few hours later, John showed up at Elizabeth's door. She opened the door not surprised to see him.

"I want to apologize for earlier. I was way out of line I shouldn't force you to have feelings for me." He said.

"Let's just put it in the past, okay?" Elizabeth said.

"You remember went I was attacked by that stupid bug?" He let it slip.

"The Iratus bug?" she asked. She didn't even realize that he had his memories.

"Yeah, that one." He said. "You know when I thought I was going to die. Yeah, well, I wanted to tell you something. I couldn't really tell you in the infirmary with Rodney, Teyla and Ford there. I wanted to though."

"What was it?" she asked.

"It was nothing now." He said.

John managed to get a few steps away before Elizabeth called out his name.

"Do you have them all back?" she asked.

"Yes." He said with no hesitation.

Elizabeth stepped forward. She kissed him. Tears were seeping from her closed eyes. John kissed her back. He pulled her closer to him.

The only reason the kiss had broke was because the both heard approaching footsteps. Two sergeants walked by. It looked as if Colonel Sheppard and Dr. Weir were just talking.

As soon as they were out of sight, Elizabeth pulled John into her quarters. The door closed behind them.

She pulled him in for a kiss. He pulled her closer to him.

They broke off.

"John…I was… we can't…" she said, out of breath.

"Yes, we can. We can keep it a secret until you are comfortable with it." John said.

"I don't know if I will be comfortable with it." She said.

He started kissing her neck.

"John, do you think it is right for us to be doing this?" Elizabeth asked. "What if something happened? Would one of us have to leave Atlantis?"

"Liz, don't worry about that now. We'll figure it out later." He said. She forced him to stop kissing her when he said 'Liz.' She just looked at him with a little smile. "What? Too soon?" She just shook her head and smiled.

He slowly laid her on to the bed. They stared into each other's eyes, both smiling.

_ShweirShweirShweir_

The next morning, Elizabeth woke up with a blurry memory of the night before. She remembered kissing John, talking to him, and that was it. She looked to her side, no on was there. She was safe from her feeling. Elizabeth eventually got up. She got read for the day.

She went to the cafeteria for breakfast. She got some food and her first cup of coffee.

She looked around for an open seat. She saw John, he was waving her over. All she wanted was not to sit near him, but her feet moved her in his direction.

"Good Morning, Rodney, John." She acknowledged both men.

"I heard something about new security protocols." John said.

"Yes, Rodney was upgrading them to detect the Wraith sooner." She said. "We are going to go over this at the conference this afternoon."

That afternoon, at the conference, Dr. Weir had a few announcements. John was normally late. He walked in late.

"We would like to thank Major Lorne for filling in for Colonel Sheppard while he was not able to work. Colonel Sheppard is now back on duty. He has made a full recovery."

Rodney spoke next. "The sensors have detected no Wraith ships as of yet. The sensors have been extended by double. It's actually a funny story. I was inspired by the Asgard." He was cut off.

"Rodney." John yelled. "There are many more important things then your stories."

"Sorry." He said.

"Now, the last planet Major Lorne, Teyla, and Ronan visited was in habited with traders very interested in trading with us." Dr. Weir explained.

"Yes, I have traded with the Capetans once before. They have wonderful craftsmanship and the traders are very gracious. I've only traded with them once because of their high-quality work. It would be beneficial for us to trade with them." Teyla explained.

"Do they have anything we need?" John asked.

"Several useful items." Teyla responded.

"Okay, take a team." Dr. Weir said. "if that is all, meeting adjourned."

Elizabeth stayed behind. She was shuffling through several sets of papers. She was startled when she heard footsteps in the room.

"John, you scared me." She said.

"Sorry, I didn't mean to." He said. "About everything that happened, I should take full responsibility. I was the one who pursued it. It was all my fault."

"No, it wasn't." She said. The doors to the conference room were closed to make the conversation a little more private. "I take equal responsibility and you shouldn't feel bad for what happened."

"I don't feel bad, I feel like I'm pressuring you." He said.

"You're not." Elizabeth said.

She stood up from where she sat and stood up in front of him. "I would have stopped this by now if you were pressuring me."

"So where do we go from here?" he asked.

"Dinner?" she suggested.

"Where?" he asked.

"Your balcony?" She suggested.

"Okay." He agreed. "1900 hours." He shouted as he walked away.

_ShweirShweirShweir_

Elizabeth arrived at John's living quarters at exactly 1900 hours.

"Prompt, very prompt." He said, jokingly as the door opened. She stepped inside.

Elizabeth was holding a bottle of wine. She handed it to John to pour.

"I have some news." She said as they sat don't to dinner. "Did you make all of this?"

"Most of it. I got a couple things from the cafeteria." He said. "So, what's your big news?"

"I have to go back to Earth soon. They need my help with some things at the SGC." She said.

"Oh." He said. "That's good."

"You're such a bad liar." She let out a laugh.

"I don't want you to leave, Liz." He said quietly.

"Maybe we could arrange you to come as security." She said.

"But Atlantis?" He questioned.

"We've both left before. Rodney and Major Lorne can take care of things until we get back." Elizabeth said.

"Yeah." He said with higher hopes.

"I was thinking maybe Teyla and Ronan could come too. They've both never seen Earth. Plus, they deserve a little r & r." Elizabeth said.

They finished their dinner. By the end of the meal, they were staring into each other's eyes.

Elizabeth stood up still staring into his eyes. It was like they were reading each other's mind. He stood up as well.

Their bodies got closer and closer. Clothes were slowly coming off.

He was kissing her neck when the door chimed.

"Damn it!" John shouted.

Elizabeth picked up her shirt and ran out onto the balcony without a word.

John put his shirt on and opened the door.

"Are you alright?" Rodney asked.

"You came all this way to ask me that?" John asked.

"Oh no. I heard you shout 'damn it.' Anyways, I couldn't reach you on the lead set." Rodney said.

"There was a point to that." He said.

"Yes, I see." Rodney said. "I thought you should know that a Wraith hive ship is only a few days away."

"Do they know were here?" John asked.

"Not yet. I wouldn't have bothered you if I could find Elizabeth." Rodney said.

"Rodney, go to the control room and I'll find Dr. Weir." John said. Rodney left. The door closed.

"Elizabeth." John called. "The sensors picked up Wraith."

"I know, I heard." Elizabeth said.

They both left his quarters.

Rodney met them as soon as they got to the control room.

"Good, your both here." Rodney said.

"What do you have?" Elizabeth asked.

"Wraith ships. Two, maybe three. They're headed this way." Rodney said.

"How long do we have?" Dr. Weir asked.

"A couple of days." He said.

"How long do we have to they pick us up on sensors?" She asked.

"Twelve hours." Ronan said as he entered the control room.

"Are you sure?" Dr. Weir asked.

"Yes." Ronan said. "I'll be ready for them when they get there."

"Hopefully it won't come to that." Dr. Weir said. "But we do have to have a plan. Rodney tell me if there are any changes."

She left to go to her office. John followed.

"We should evacuate the city. It's our only chance." She said.

"We just can't leave. If we leave, the Wraith will be more powerful because they will have captured the city. They'll be unstoppable." John argued.

"That leaves us with the issue of sinking the city. We can leave it the way we found it. Leave it for the next generation." Elizabeth suggested.

"What would we do? Just go to another planet? Live out our lives alone?" He asked.

"The Daedalus is due back any day now. We can transport as many people as we can and the rest can gate to another world and wait for the Daedalus to return. Or possible we can gate directly to Earth." She explained. Her voice was full of fear and worry.

"Liz, we're going to get through this." John said with confidence.

"I know, I'm just worried. Atlantis has become home, I just don't know if I will be able to leave." Elizabeth said. She stood up and walked around the desk. She leaned on the desk in front of him.

John held Elizabeth. "We don't have to leave." John whispered.

John and Elizabeth jumped apart. She wiped the tears from her eyes and straightened her posture.

"Rodney." She said.

"Umm…yes…the Daedalus has returned. I just thought you should know." Rodney was confused. "Wait, what's going on?"

"Rodney, what were going to tell you cannot leave this room, do you understand me?" John said. Rodney closed the door.

"We're seeing each other, in private. We really don't want this to spread throughout the city. Can we trust you with this Rodney?" Elizabeth said.

"Yes…yes…my lips are sealed." Rodney said.

"Now, business. What are we going to do " John asked both Rodney and Elizabeth.

"We could always use the cloaking device like we did the last time. We could turn it on right before they are able to detect us." Rodney suggested. "We'd be without a shield, but we could 'fool' them."

"That's the best idea we have. Start working on it. Get as much power to the cloaking device as you can. Take it from where ever you need to." Elizabeth said. Rodney left the room. "Oh. I completely forgot."

"What?" he asked.

"I still have to go back to Earth." She said.

"The city will be okay without you." He said.

"No, I can't leave. I think General Landry will understand, given the circumstances." Elizabeth said.

John didn't say anything. He didn't know what to say.

"It's late, you should get some rest." She said as she shuffled through some papers.

"Me? What about you? You need rest too." John asked.

"There's too much to be done." She said.

"It will all be here in a couple hours. That's all I'm asking. Just take a couple hours to sleep." He said.

"Alright, I guess it couldn't hurt." She said.

"She and John stood up and walked out of her office together. They arrived at his quarters. They both laid down. He put his arms around her and held her close. They both fell fast asleep.

_ShweirShweirShweir_

Elizabeth woke up. It had been seven hours since she fell asleep. What happened to that couple of hours? She got up and left without waking John.

"Rodney, how far off are they?" she asked.

"It seems they've slowly down a bit. It will be a bit longer before they sense us." Rodney said.

"How much longer?" Dr. Weir asked.

"Four, maybe five hours tops." Rodney said.

Colonel Caldwell, who had arrived several hours before, was watching Dr. Weir.

"Colonel, I want the Daedalus up and running within the hour. I want you to be ready to go at a moments notice." She said. "I want as many non-essential personnel as you can on the Daedalus back to Earth."

"I'm ready whenever you are." He said.

"Attention all Atlantis Personnel. I am sure you are aware of the Wraith ships head this way. All non-essential personnel will board the Daedalus and return to Earth within the hour. As for the military, only teams one, two, three, and four will remain behind." Dr. Weir said over the headset.

"Teyla, will you contact the Athosians. Make sure they are aware of the attack. They are welcome to come to Atlantis or they can gate to another planet until its safe." Dr. Weir said.

"I will do so." She said.

"Ronan, we're going to need your need here." He didn't say anything. He looked at Teyla before she left, then approached the consol in the control room.

Ronan explained how the Wraith would attack to Rodney while Dr. Weir wrote her letter to General Landry.

There was a knock at the door. It was John.

"Are you okay?" You haven't been looking well for the last couple of days." John asked.

"I'm fine. I guess the worrying and the lack of sleep have just caught up with me." She said.

"Maybe you should see Carson, just to be sure." He said. John got up and walked over to the military still left on Atlantis to brief them.

_ShweirShweirShweir_

Elizabeth did go see Carson. He was the only medical personnel left on Atlantis.

"Carson, do you mind giving me a quick physical to ensure Clolonel Sheppard that I am fine.?" She asked.

"Why would he be concerned if you were physically fit or not?" Carson asked.

"He said I haven't been looking too well the last couple of days." She said.

"Okay. Just answer these questions." Carson handed her a questionnaire. She answered all the questions until she got to number 10. Have you been sexually active? She couldn't just lie to Carson. She circled the yes and continued to answer the questions. She handed Carson the questionnaire.

"Okay." He said as he reviewed the questionnaire. "You have been sexually active? With who? Sorry don't tell me, it doesn't matter. Have you felt any nausea?"

"I have felt a little bit sick, but I've never thrown up." She said.

"Have you had any back problems?" he asked.

"No." she said.

"Have you had any fevers lately?" he asked. She said no.

"Okay. I just want to run a few test." He said. "They're very simple tests. They'll just take a few minutes."

A few minutes later, Carson announced he knew what was wrong with Elizabeth.

_ShweirShweirShweir_

What will happen? What is wrong with Elizabeth? Is she okay? Will the Wraith finally attack?


	3. Chapter 3

Thank You to **delta1999x**, **ilovedanieljackson**, **Kyrah-Lee** (Lexa), **Jenn R**, **mentalmichael**, **Tinuviel Undomiel**, **Mlle Lambert**, **Yarrharr**, **Dreamer20715**, **EmmyLou32**, **tracey**, and **Astraldust** for the reviews.

**delta1999x**- Sorry for all the confusion.

**ilovedanieljackson**- Nope, no time loop.

Kyrah-Lee- Thanks for telling me, I didn't realize it until I was in class. Everything is right now. 

**Jenn R**- I'm trying to get all chapters out as soon as possible. I still have to write/finish chapter 3. It was only luck that I had already written chapter 2 when I first posted. Have I left you with a good question? Is she pregnant? I think everyone wants to know.

**mentalmichael**- I actually chuckled a bit when reading your review. I have to add the 'Typical Ronan.' We all love typical Ronan. That part reminded me of Instinct. You are the only person to ask what is wrong with Elizabeth. That's so great.

**Tinuviel Undomiel**- I think everyone is hoping she will be well in nine months. I'm hoping too.

**Mlle Lambert**- Have you reviewed to one of my stories before? Your name seems familiar. I'm glad you like my story. I was looking at you profile. Its sounds like me, at least most of the way down.

**Yarrharr**- haha, that's so funny. Is she pregnant? Is it John's? And is it a Wraith baby? I had to in put Ronan/Teyla (I affectionately refer to it as Reyla). Originally, I had Shweir and Ronan/Teyla, but had to cut it down. I always love to hint at Ronan and Teyla, I'll probably have some more in the near future.

**Dreamer20715**- Thank you, I'm glad you like it.

**EmmyLou32**-Thank you. I don't really see myself as a talented writer. I just write, but thank you anyway.

**tracey**- I'm glad that you enjoyed my story so far.

**Astraldust**- Here you are…the next and last chapter.

Does anyone else but me think John is getting a lot of action in season two? I mean first Teyla in Conversion. Then the ascending woman in Epiphany. Also that Ancient woman in the Tower. And Elizabeth in the Long Goodbye.

Chapter 3

"What is it Carson?" Elizabeth asked.

"You're pregnant." He said.

"Pregnant?" she swallowed.

"Yes, my dear." Carson said. "Now, what are you going to do about it?"

"What?" she asked. "Sorry, I wasn't paying attention."

"What are you going to do about it?" He repeated.

"I don't know, what are my options?" she asked.

"Termination. Taking the child back to Earth. Giving the child to the Athosians. Keeping it." Carson listed.

"I'll think about it." She said as she left.

'Pregnant.' She thought. 'How am I going to tell him? Should I even tell him? I could always have the child terminated.'

Elizabeth was walking down one of the corridors when she ran into Teyla

"Hello, Dr Weir." She said. "How are you today?"

"Good." Dr. Weir lied. 'Completely freaked out, scared.'

"Is anything wrong?" Teyla asked.

"No, not at all." She lied.

Teyla knew something was wrong, but she didn't inquire any further.

Elizabeth continued to walk to her office.

Both Rodney and John were waiting for her.

They waited before they started talking until she sat down.

"Two hours left." Rodney said.

"How long will the city be able to keep up the cloak?" Dr. Weir asked.

"It eats zed-pm power like candy. I can keep it up for two days, maybe three if we really push it and use only the necessary power for the city." Rodney explained. "But we're going to have to start looking for zed-pms again after this."

"Good. Turn the cloak on in one hour." She said. Rodney left to work on the cloak.

"I went to see Carson." She said sitting back in her chair.

"Nothing wrong. Nothing to worry about." John said.

Elizabeth said nothing.

"Nothing to worry about, right?" John asked. Now he was starting to get worried. "Right?"

"Yeah, nothing." She said. She didn't look at him once.

"Now I know something is wrong." He said. "What is it? I can handle it."

"I don't think you can." She said.

"How do—" he was cut off.

"I'm pregnant." She said.

"What? How? When?" he couldn't say anything more.

"John." She sighed.

"I'm sorry, I should be happy, right?" He said. "I'm just in shock. I mean, we just started seeing each other. How? What are we going to do?"

"I think the biggest problem in word of mouth control. Rodney knows and I think Carson is starting to put the pieces together and Teyla. She knows something is different." Elizabeth explained. "As soon as I start to show, the rumors will fly. I still need to figure out what I'm going to do."

"What choices do you have to make?' he asked.

"What am I going to do with the child?" she asked.

"You're going to have this child. None of that abortion stuff." He said.

Yeah, I'm going to that the baby, but should I go back to Earth or stay here?" she asked.

"Don't worry, Carson can take care of everything." John said.

"I know, but I should go back to Earth to get a few things and tie up a few loose ends." She said.

"That's a good idea." He said.

---

"The Wraith had arrived. I don't think they have sensed us yet." Rodney said. "The shield is holding."

John was standing, fully armed, in the gate room with all the military personnel. They were ready for any attack on the city.

"The Wraith weapons are powering up." Rodney said.

"What? Have they picked us up yet?" Dr. Weir asked.

"No." Rodney confirmed.

The first Hive ship fired upon the second Hive ship.

"They're firing upon each other. The sects of Wraith must be feuding for any small reason." Rodney said. "They destroyed each other. Heh."

"Take down the cloak." She said. "All military personnel stand down."

Rodney did just that. The cloak went down and the shields went up.

---

The Daedalus returned three weeks later with all the personnel of Atlantis.

Elizabeth had to return to Earth. It was a business trip and a personal one too.

She had to meet with General Landry and fix things up with her family.

John pleaded with her not to go, but she had to.

She wanted John to go with her but he was convinced he had to stay in Atlantis, if the Wraith returned.

Elizabeth convinced him to go.

"You should come. You can meet my family and I still need to get some baby things." She said.

"I can't. I don't want anything to happen to Atlantis while I'm gone." He said.

"They won't. We'll leave Atlantis in capable hands. Rodney and Major Lorne can take care of things for a little while." Elizabeth said.

"I don't know." He said. "If we go, can we do something that I want?"

"Sure, Anything." She said.

John stood up when she said 'yeah.'

He got down on both knees to be eye and eye with her. "Maybe we could…get married?"

"Are you asking me what I think you're asking me?" She asked.

"Yeah. Well, it's more of a suggestion, really." He said. "Liz, I love you. I've loved you since we've been here. We're having a child together. I want to be with you for the rest of my life with you. Make me happy. Marry me?"

"Yes, John." She replied. She kissed him.

That day, they boarded the Daedalus. Teyla and Ronan came along. Elizabeth thought they could use some well-deserved time off.

Three week later, the Daedalus arrived at Earth.

The passengers were beamed down to Earth, Cheyenne Mountain.

General Landry was there to greet them. "Hello, Doctor, Colonel. It's good to see you again. You must be Teyla and Ronan. On behalf of Earth, Welcome!" The General shook their hands. John gave Ronan a funny look.

"Thank you, General." She said.

"Now, if there are no objections, we can debrief." The General said.

"Yes, sir." John said.

"Why do we have to debrief?" Ronan asked John.

"Standard Procedure." He said.

"Sir, SG-1 is waiting for you in the briefing room." A Sergeant said.

"Well, okay." He said. "Let's not keep them waiting."

They climbed the stair to the briefing room.

"SG-1, you know Dr. Weir and Colonel Sheppard. And this is Teyla and Ronan." General Landry said. "Teyla, Ronan, this is Colonel Carter, Colonel Mitchell, Dr. Jackson, Teal'c."

"You are not human." Teyla said.

"No, I am not. I am a Jaffa." Teal'c said. Teyla didn't know that term, but the must be allied with Earth. She had heard it only before when the 'goa'uld' was in Colonel Caldwell.

John looked at Mitchell, they knew each other. They had gone to flight training together, but never really got along. Mitchell was busy staring at Teyla. She didn't really notice. Ronan glared at Mitchell.

"SG-1. Your mission to P6G-452 is low profile. That means not shoot and no promoting Earth."

"Yes, sir." The Colonel said.

"It was nice meeting you Teyla, Ronan." Sam said.

"Yes, if you're still here when we get, I would like to know more about your culture." Daniel said.

After their debriefing, the four left Cheyenne Mountain. They went to Colorado Springs for the day.

Teyla and Ronan didn't know about John and Elizabeth and vice versa. It would eventually have to come out about it.

They ate at one of the diners in town. They walked around for a while. Elizabeth came across a small baby store.

"We should tell them. I want to go in." She whispered to John.

"Teyla, Ronan, I know this isn't the best time to tell you, but I'm pregnant." Elizabeth announced.

"Congratulations, Dr. Weir!" Teyla said hugging her.

"So, who's the father?" Ronan asked. Teyla glared in his direction.

"I am." John said.

"Then I owe a 'Congratulations' to you too." Teyla said.

"Can we keep this between us? We don't want it spending too much around Atlantis before it has to." She asked.

"Of course." Teyla said.

Elizabeth went into the store with John, Teyla, and Ronan.

They looked around.

"Why do children need so much stuff?" Ronan asked.

"People like to shower their children in gifts when they are born. It's a way of celebrating their birth." Elizabeth explained.

"My people celebrate the birth of a child, but we only supply them with the things they will need for life." Teyla said.

The store clerk looked up from the counter as Teyla talked.

"Her religion." Elizabeth assured him.

The clerk paid little attention to Teyla from then on.

"We need some things." John said to the clerk.

"Oh, are you expecting?" He asked.

"Yes." Elizabeth said.

"Oh, how wonderful. Is this your first?" He asked.

"Yes." Elizabeth said.

"Is it a boy or girl?" The clerk asked.

"We don't know yet." John said.

"Oh, well in that case, green is the best way to go. It can always go both ways." The clerk suggested.

"Green. I like green." She said.

"Let's see, you'll need a crib, clothes, a changing table, bottles, pacifiers, a toy or two for learning." The clerk listed.

"The simpler the better." John asked.

"I like that crib." Elizabeth said pointing to a warm oak colored crib. It was very simple. It also came with a changing table.

"John, look at this." Elizabeth said holding a little green jumpsuit that said 'Just Like Daddy.'

"My wife made that. So many couple that are in the military are living around here now." The clerk said.

"We'll take it." John said. They picked out a few more things before leaving.

"This is a gift." The clerk told them, before ringing them up. It was a little bear with a jumpsuit on.

They took their newly bought baby things back to Cheyenne Mountain.

"You know what, we should see a football game." John said.

"Football?" Ronan asked.

"I believe it is 'the cornerstone of western civilization.'" Teyla said.

"Maybe another time. Or you could go without me." Elizabeth said.

"Okay, Liz, maybe another time. We could still see if theirs a game on." John said.

"I have to leave you three to your own." Elizabeth said.

"Why?" John asked.

"I have to go out go town." She said.

"Where?" John asked.

"Seattle." She said. "I'll be back tomorrow."

John, Teyla, and Ronan bid Elizabeth farewell at the airport. John kissed Elizabeth for the first time in public.

Elizabeth's plane landed in Seattle after a short flight.

She got into a cab to go to into the suburbs just outside of Seattle.

The cab stopped in front of a large, white Victorian-style home in the middle of the suburbs.

Elizabeth slowly walked up to the door. She stood there a minute, thinking, before she rung the doorbell.

"Hello, can I help you?" A maid said.

"Um, yes. Is Meredith Weir in?" Elizabeth asked.

"Yes, please come in." the maid said.

"Who are you?" she asked.

"The day maid, ma'am." The maid said.

"Elizabeth." Her mother said. "What are you doing here?"

"Visiting. I had some time, so I'm visiting." She said. They both sat down. The maid brought tea in.

"Why do you have a maid?" she asked.

"Maxwell insisted that I had a maid." Her mother said.

"Maxwell?" she asked.

"My husband." She said.

"Husband? I've been gone for two years and you got remarried?" she asked in disbelief.

"I had to support myself somehow." Her mother said.

"A job could do that." Elizabeth said.

"Don't be silly, dear. I don't work." He mother said.

"So, when did you get remarried?" Elizabeth asked.

"Last Year. We tried to reach you, but it's like you dropped off the face of the Earth or something."

"Yeah, something like that." She said. "How are Margy and Sharon?"

"They are over almost everyday, with their families." She said. "When are you going to start yours? You know your not getting any younger. When I heard you broke up with Simon, I was stunned."

"He broke up with me, but that's not the point." Elizabeth said. "I came to talk you about my family."

"Who is he? I want all the details." Her mother said. For the first time, her mother was happy to see her.

"His name is John Sheppard. He is in the military, the air force. He's a lieutenant colonel. We work together. It's the same project we've been working on for the last two years. That's where I've been." She explained.

"What does he look like?" Her mother asked with a snobby attitude.

"Dark brown hair, brown eyes, strong, and very good-looking." Elizabeth described John.

"When am I going to meet him?" she asked.

"He's in Colorado Spring right now." Elizabeth said.

"Have you set a date yet?" she asked.

"Actually, we have to get married really soon because we have to go back to work." Elizabeth said.

"How soon is soon?" She asked.

"Within the next five days." Elizabeth said.

"FIVE DAYS!" Her mother yelled.

"I know it's soon, but we have to go back to work." She said.

"How are you going to plan a wedding?" Her mother asked.

"Actually, we were thinking about eloping." She said.

"Eloping! No daughter of mine will elope." Her mother said.

"It's our only option." Elizabeth explained. "We'll come back and have a real wedding when we have more time."

"No, you won't. You will not marry that man." Her mother said.

"Yes, I will." She said. "And by the way, I'm pregnant. Good bye."

Elizabeth left. Her sisters were arriving as soon as she stepped out the door.

"Elizabeth?" Margy called out. "What are you doing here?"

"Visiting." She said.

"Where have you been for the last two years?" Sharon asked.

"Work." She said.

"Where?" Sharon asked.

"It's classified. Military." She said.

"Always Classified." Margy exclaimed. Her sisters walked away.

Elizabeth knew that her sister would share her mother's enthusiasm for Elizabeth news.

Elizabeth boarded a plane back to Colorado. She returned to the base.

"Back so soon?" John asked.

"Let's just say, we didn't get along too well." She explained.

"What happened?" he asked.

"She forbid me to marry you." She explained.

"What? She hasn't even met me yet?" she said. "I can be very charming."

"I know. I told her that we had to get married soon and she flipped out." She explained.

---

A few days later, Elizabeth and John got married. Witnesses to this were Ronan and Teyla.

The minister presiding over the ceremony was Elizabeth minister as a child.

"Do you Elizabeth Weir take John Sheppard to you your lawfully wed husband?" he asked.

"I do." She said.

"Do you John Sheppard take Elizabeth Weir to you your lawfully wed husband?" he asked.

"I do." He said.

"I now pronounce you husband and wife. You may kiss the bride." He said.

He did just that. He gave her a tender kiss. They were now married.

She was now Dr. Elizabeth Sheppard, but at Atlantis, it would have to stay Dr. Weir for the time being.

After the ceremony, Teyla and Ronan gave their congratulations and left the newlyweds alone.

The couple returned to Cheyenne Mountain. They had to leave the next day.

They laid in their bed. John had his hand over her stomach.

"My family." He whispered. "I want it to be right this time."

Elizabeth knew of John's past. She knew his parents had died when he was young and that he was separated from his brother early on. He had never found his brother after he was adopted. He was all alone, but not he had a family.

They drifted to sleep.

Again, they boarded the Daedalus and returned to Atlantis three weeks later.

The city was still in one piece. And I looked better than ever.

Elizabeth and John decided to start moving things into the larger quarters. Since, no one knew, they would have to do it in secret.

---

At about three months, Elizabeth started to show. As predicted, the rumors started to fly.

"Have you seen Dr. Weir lately?" One Sergeant. said.

"Yeah, I wonder who the father is?" Another Sergeant. Said

"It could be Dr. McKay." The first sergeant said. "They've been spending a lot of time together. Their always together."

"Maybe its Colonel Sheppard." The second Sergeant said. They have always been close and they have always had feeling for each other. Everyone can tell.

"If its one of them, it could be anyone." Another sergeant said. "Maybe Zelanka." another Sergeant said.

"Zelanka? Isn't he married?" the first Sergeant asked.

"I don't know, but no one is married out here." The second Sergeant said. "What about Major Lorne? He has always been loyal to her."

"What about Carson?" the first Sergeant asked.

"Isn't he with Lieutenant Cadman?" The second Sergeant asked.

"But that could always be a cover." A Sergeant said.

The rumor did fly. Elizabeth was paired with every male at Atlantis.

---

At about six months, the news had come out. In a newsletter, Elizabeth squashed all rumors.

All Atlantis Personnel:

It is clear to see that I am pregnant. The rumors of the father being Dr. Beckett, Dr. Zelanka, Dr. McKay, Major Lorne, or any other man that I have been put with are false. They truth is, the father is Colonel Sheppard. While on Earth, we got married. I have prolonged making this announcement as long as I could. There will be a name change. Thank you for ceasing all rumors.

Dr. Elizabeth Sheppard

After the letter was sent out, John came to see Elizabeth.

"Rodney just told me 'congratulations' and said it was funny to pair you and him together." He said. "So I told him he had a piece of pulp in his teeth. He ran to the infirmary."

"I heard the city is buzzing about it." She commented.

"Yeah, they are. Is that why you're hiding out here?" he asked.

She nodded her head. "Plus, my feet are swollen."

"Let's go eat." He suggested.

"You go." She said. "The Cafeteria has already sent two plates of food up. We can't eat anymore."

"You're calling yourself 'we' now?" He asked.

"This child has a mind of its own." She said. "It reminds me of someone I know." She smiled at him.

John laughed. "Liz, don't you think its time that we found of the sex of the child."

"I suppose we should. I really don't like calling it 'it'." Elizabeth said.

Elizabeth and John went to see Carson.

"We want to know the sex of the child." Elizabeth asked.

"Okay, lay here." Carson said. "Laura was relieved when your letter came out. She thought I was lying to her."

"Is Rodney still here?" John asked, looking around.

"No." He said. "Wait, was it you that sent him here?"

"Sorry, I had to." John said.

"Okay, your child is a ." Carson said. "Boy."

"A boy, we're going to have a son." John said. He kissed her.

They left the infirmary very happy. They were in live, they were having a child, what more could they want?

They finally were able to move into the family quarters living space. They had been moving things in slowly for the past three months.

---

Three months had gone by. Elizabeth was nine months pregnant. She hadn't gone into labor, but she would be soon. John was accompanying her everywhere so he would be there when it happened.

She found it unnecessary, but she knew he cared. She told him that he should go on missions and that she would be fine. Actually, it was more of an order.

He had to follow orders. He kissed he and left. He had just rounded the corner when he heard, "John!" yelled.

It was Elizabeth. John came running back.

John." She said. She was bending over leaning against the wall.

"Liz, what's wrong?" he asked. 'Stupid question,' he thought.

"He's coming. And at full force too." Elizabeth said.

"Carson," John called on the headset.

"What is it, Colonel?" Carson replied.

"He's coming." John said.

"Okay, bring her down here now." Carson said.

"We're on our way." John said.

They made their way to the infirmary.

"Change into this." Carson said as he handed her a gown. "you can change in the next room."

Elizabeth came out of the next room, changed.

"Lay down here and I'll hook you up to the machine." He said. Carson hooked her up to the monitoring machine and to an IV. "I want to know when you have any contractions."

"Carson!" she yelled. She grabbed John by the shirt and screamed.

"Is this supposed to happen?" John asked.

"Well, it is common for the mother to blame the father for all the pain in the birth process." Carson explained.

"It's coming, Carson." She yelled. "Get this thing out of me."

"Liz, Carson is doing all he can to hurry this." John said.

"Don't say another word. Your the one that did this to me." She yelled. "Don't touch me."

John said no more.

After a contraction, she yelled out, "John!" She grabbed his hand and squeezed it tight. "I'm so sorry. I didn't mean to yell at you. I'm sorry, I love you."

"Liz, don't worry about it. It's normal." He said. "I love you too, Liz." He kissed her forehead. His hand was starting to turn purple.

After several hours, Elizabeth finally did have her baby.

He slept in her arms.

"What are we going to name him?" John asked.

"Eion." She said.

"Eion, I like that." He said. "Or we could name him John."

"No." She said.

"Then Eion it is." John agreed.

"Eion John Sheppard." She said.

"I love you, Liz." John said.

"I love you too, John." Elizabeth said.

Rodney, Teyla, Carson, and Ronan came into see the happy family.

"Congratulations Dr. Sheppard, Colonel Sheppard." Teyla offered. "I want your child to have these. They are a gift from the Athosian people."

She handed John a hand-carved box. It contained little knickknacks and toys from her people.

"Thank you, Teyla." Elizabeth said.

"So, what did you name the little bugger?" Carson asked.

"Eion." Elizabeth said.

Atlantis was buzzing about the good news.

THE END!

Did you like it? Was it good enough?


End file.
